I would be interested in seeing hg19 UCSC tracks like repeat-masked regions, tandem repeats, microsatellites, retroposed genes, segmental duplications, multiz alignments, you name it. These tracks would help me in quickly assessing the credibility and importance of short read alignments and detected variants.

2 answers

GenomeBrowse 2.0 has been released! You can download the most recent installer from our website.

Included in the new version is the ability to add data sources to GenomeBrowse. We have added a new Covert Wizard that can take any any tabular file and convert it to TSF (Golden Helix tabular file format) so it can be visualized in GenomeBrowse. So for UCSC annotations if the data can be downloaded in some form of delimited text (including BED files) then they can be converted and visualized in GenomeBrowse. You can launch the convert wizard by going to File > Convert.

Thank you for your request. We are constantly working on creating a more comprehensive annotation source library.

We are in the process of updating our annotation track writer so that we can create new tracks more efficiently and quickly have them available from our data server. Once this is complete we will start updating our available tracks. I have added the tracks you mentioned to our list (Segmental Duplications is already available!) and we should begin working on them after the first of the year.

Additionally we are working on creating a tool that will allow the user to create their own annotation tracks from a variety of file types (GTF, FASTA, etc.), we will be implementing this tool in our analysis software SVS first but will then make it available in our stand-alone GenomeBrowse software.

Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.